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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-21833291-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21833291&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"hgvs_c": "c.11075C>T",
"hgvs_p": "p.Thr3692Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_001291860.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 1279,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1791,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "HSPG2-related disorder,Lethal Kniest-like syndrome,Schwartz-Jampel syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:5 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.026100903749465942,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "T",
"aa_start": 3691,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 11165,
"cds_end": null,
"cds_length": 13176,
"cds_start": 11072,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 80,
"exon_rank_end": null,
"feature": "NM_005529.7",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11072C>T",
"hgvs_p": "p.Thr3691Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374695.8",
"protein_coding": true,
"protein_id": "NP_005520.4",
"strand": false,
"transcript": "NM_005529.7",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "T",
"aa_start": 3691,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 11165,
"cds_end": null,
"cds_length": 13176,
"cds_start": 11072,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 80,
"exon_rank_end": null,
"feature": "ENST00000374695.8",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11072C>T",
"hgvs_p": "p.Thr3691Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005529.7",
"protein_coding": true,
"protein_id": "ENSP00000363827.3",
"strand": false,
"transcript": "ENST00000374695.8",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4392,
"aa_ref": "T",
"aa_start": 3692,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14344,
"cdna_start": 11168,
"cds_end": null,
"cds_length": 13179,
"cds_start": 11075,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 80,
"exon_rank_end": null,
"feature": "NM_001291860.2",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11075C>T",
"hgvs_p": "p.Thr3692Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278789.1",
"strand": false,
"transcript": "NM_001291860.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 305,
"aa_ref": "T",
"aa_start": 68,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 921,
"cdna_start": 205,
"cds_end": null,
"cds_length": 919,
"cds_start": 203,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000635682.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.203C>T",
"hgvs_p": "p.Thr68Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489161.1",
"strand": false,
"transcript": "ENST00000635682.1",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4574,
"aa_ref": "T",
"aa_start": 3874,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14890,
"cdna_start": 11714,
"cds_end": null,
"cds_length": 13725,
"cds_start": 11621,
"consequences": [
"missense_variant"
],
"exon_count": 102,
"exon_rank": 85,
"exon_rank_end": null,
"feature": "XM_011541318.3",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11621C>T",
"hgvs_p": "p.Thr3874Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539620.1",
"strand": false,
"transcript": "XM_011541318.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4557,
"aa_ref": "T",
"aa_start": 3857,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14839,
"cdna_start": 11663,
"cds_end": null,
"cds_length": 13674,
"cds_start": 11570,
"consequences": [
"missense_variant"
],
"exon_count": 101,
"exon_rank": 84,
"exon_rank_end": null,
"feature": "XM_047419080.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11570C>T",
"hgvs_p": "p.Thr3857Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275036.1",
"strand": false,
"transcript": "XM_047419080.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4556,
"aa_ref": "T",
"aa_start": 3856,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14836,
"cdna_start": 11660,
"cds_end": null,
"cds_length": 13671,
"cds_start": 11567,
"consequences": [
"missense_variant"
],
"exon_count": 101,
"exon_rank": 84,
"exon_rank_end": null,
"feature": "XM_047419090.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11567C>T",
"hgvs_p": "p.Thr3856Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275046.1",
"strand": false,
"transcript": "XM_047419090.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4456,
"aa_ref": "T",
"aa_start": 3756,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14458,
"cdna_start": 11282,
"cds_end": null,
"cds_length": 13371,
"cds_start": 11267,
"consequences": [
"missense_variant"
],
"exon_count": 98,
"exon_rank": 81,
"exon_rank_end": null,
"feature": "XM_017001120.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11267C>T",
"hgvs_p": "p.Thr3756Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856609.1",
"strand": false,
"transcript": "XM_017001120.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4455,
"aa_ref": "T",
"aa_start": 3755,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14455,
"cdna_start": 11279,
"cds_end": null,
"cds_length": 13368,
"cds_start": 11264,
"consequences": [
"missense_variant"
],
"exon_count": 98,
"exon_rank": 81,
"exon_rank_end": null,
"feature": "XM_047419091.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11264C>T",
"hgvs_p": "p.Thr3755Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275047.1",
"strand": false,
"transcript": "XM_047419091.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4439,
"aa_ref": "T",
"aa_start": 3739,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14407,
"cdna_start": 11231,
"cds_end": null,
"cds_length": 13320,
"cds_start": 11216,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 80,
"exon_rank_end": null,
"feature": "XM_017001121.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11216C>T",
"hgvs_p": "p.Thr3739Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856610.1",
"strand": false,
"transcript": "XM_017001121.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4438,
"aa_ref": "T",
"aa_start": 3738,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14404,
"cdna_start": 11228,
"cds_end": null,
"cds_length": 13317,
"cds_start": 11213,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 80,
"exon_rank_end": null,
"feature": "XM_017001122.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.11213C>T",
"hgvs_p": "p.Thr3738Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856611.1",
"strand": false,
"transcript": "XM_017001122.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1602,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000471322.2",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "n.1427C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000471322.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149159881",
"effect": "missense_variant",
"frequency_reference_population": 0.00079237536,
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"gnomad_exomes_ac": 1178,
"gnomad_exomes_af": 0.000805846,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_ac": 101,
"gnomad_genomes_af": 0.000663095,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 7,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Lethal Kniest-like syndrome|Schwartz-Jampel syndrome|not specified|Lethal Kniest-like syndrome;Schwartz-Jampel syndrome|not provided|HSPG2-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.719,
"pos": 21833291,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.424,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001291860.2"
}
]
}